Among the most common and debilitating human birth defects are those that affect craniofacial tissues. The last decade has witnessed the identification of numerous candidate regulatory genes that are expressed in regionally restricted patterns in the craniofacial primordia. Among these are homeobox transcription factors that include the D1x gene family. In mammals there are three Type A D1x genes (2,3,5) and three Type B D1x genes (1,6,7). These genes are expressed in nested patterns in the primordia of the branchial arches as well as the olfactory and otic apparati. We have made loss-of-function mutations of D1x1, D1x2, D1x1&2 and D15 in the mouse and found that these genes are essential for normal skeletal morphogenesis of the jaw apparatus and teeth, as well as the nasal and otic capsules. Comparison of the D1x-expression patterns with the morphological defects seen in the D1x mutants suggests that there is a D1x combinatorial code that specifies regional morphogenesis of the branchial arches and olfactory and otic apparati. To evaluate our combinatorial model of D1x function, we are studying craniofacial molecular and tissue patterning in D1x compound mutants. In addition, we will study the cellular and molecular mechanisms through which the D1x genes regulate craniofacial development.